miR prediction:
Web Servers:
Downloadable:
- open in new windowmiRFinder A freeware for microRNA prediction
- open in new windowtriplet-SVM classifier
Target Prediction:
- open in new windowTargetScan - Prediction of microRNA target
- open in new windowPITA - predict microRNA-target interaction or target seqs
- open in new windowPicTar an algorithm for the identification of microRNA targets
- open in new windowmicroRNA.org - includes expression information
- open in new windowDIANA Tools for miRNA pathway analysis
- open in new windowRNAhybrid - tool for finding the minimum free energy hybridisation of a long and a short RNA
- open in new windowmiRNA - Target Gene Prediction at EMBL (drosophila)
- open in new windowmiRanda - the program behind microRNA.org, which can be downloaded and used with any dataset
- open in new windowmiRNAMap
- open in new windowMAMI - human target prediction in Harvard, with option to send results to DAVID
- open in new windowmiRWalk - Database of human, mouse, rat miR-target interactions
- open in new windowMicroCosm - precomputed target prediction accross many species
Other programs:
- open in new windowDiana-mirPath pathway analysis of putative target lists of one or multiple microRNAs
- open in new windowSylamer overrepresentation of sequences in expression data
- open in new windowmiRGator An integrated system for functional annotation of microRNAs
- open in new windowGenMir++ - combining miR and mRNA expression data
- open in new windowMMIA - microRNA and mRNA Integrated Analysis
- New open in new windowRNA22 predictions for Homo Sapien, Mus Musculus, Drosophila, and C. Elegans
Databases:
- open in new windowDIANA-Tarbase provides hundreds of thousands of high quality manually curated experimentally validated miRNA:gene interactions, enhanced with detailed meta-data
- open in new windowmiRBase a searchable database of published miRNA sequences and annotation
- open in new windowmiRWalk - Database of human, mouse, rat miR-target interactions for gene regulation by mammalian micro-RNAs
- open in new windowmiRNAMap
- open in new windowsmall RNA in plants - database of sequenced small RNAs in many plant species
- open in new windowmir2disease - dtabase of miRNA disregulation in human disease